Merge branch 'features/JAL-2885UniprotHttps' into releases/Release_2_10_4_Branch

[jalview.git] / src / MCview / PDBChain.java

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index f2dd3d0..29b994e 100755 (executable)
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -41,11 +41,6 @@ public class PDBChain
 {
   public static final String RESNUM_FEATURE = "RESNUM";
 
-  /**
-   * SequenceFeature group for PDB File features added to sequences
-   */
-  private static final String PDBFILEFEATURE = "PDBFile";
-
   private static final String IEASTATUS = "IEA:jalview";
 
   public String id;
@@ -83,10 +78,10 @@ public class PDBChain
 
   public String pdbid = "";
 
-  public PDBChain(String pdbid, String id)
+  public PDBChain(String thePdbid, String theId)
   {
-    this.pdbid = pdbid == null ? pdbid : pdbid.toLowerCase();
-    this.id = id;
+    this.pdbid = thePdbid == null ? thePdbid : thePdbid.toLowerCase();
+    this.id = theId;
   }
 
   /**
@@ -167,15 +162,58 @@ public class PDBChain
   }
 
   /**
-   * copy over the RESNUM seqfeatures from the internal chain sequence to the
+   * Annotate the residues with their corresponding positions in s1 using the
+   * alignment in as NOTE: This clears all atom.alignmentMapping values on the
+   * structure.
+   * 
+   * @param as
+   * @param s1
+   */
+  public void makeExactMapping(StructureMapping mapping, SequenceI s1)
+  {
+    // first clear out any old alignmentMapping values:
+    for (Atom atom : atoms)
+    {
+      atom.alignmentMapping = -1;
+    }
+    SequenceI ds = s1;
+    while (ds.getDatasetSequence() != null)
+    {
+      ds = ds.getDatasetSequence();
+    }
+    int pdboffset = 0;
+    for (Residue res : residues)
+    {
+      // res.number isn't set correctly for discontinuous/mismapped residues
+      int seqpos = mapping.getSeqPos(res.atoms.get(0).resNumber);
+      char strchar = sequence.getCharAt(pdboffset++);
+      if (seqpos == StructureMapping.UNASSIGNED_VALUE)
+      {
+        continue;
+      }
+      char seqchar = ds.getCharAt(seqpos - ds.getStart());
+
+      boolean sameResidue = Comparison.isSameResidue(
+              seqchar, strchar, false);
+      if (sameResidue)
+      {
+        for (Atom atom : res.atoms)
+        {
+          atom.alignmentMapping = seqpos - 1;
+        }
+      }
+    }
+  }
+
+  /**
+   * Copies over the RESNUM seqfeatures from the internal chain sequence to the
    * mapped sequence
    * 
    * @param seq
    * @param status
    *          The Status of the transferred annotation
-   * @return the features added to sq (or its dataset)
    */
-  public SequenceFeature[] transferRESNUMFeatures(SequenceI seq,
+  public void transferRESNUMFeatures(SequenceI seq,
           String status)
   {
     SequenceI sq = seq;
@@ -184,10 +222,11 @@ public class PDBChain
       sq = sq.getDatasetSequence();
       if (sq == sequence)
       {
-        return null;
+        return;
       }
     }
-    /**
+
+    /*
      * Remove any existing features for this chain if they exist ?
      * SequenceFeature[] seqsfeatures=seq.getSequenceFeatures(); int
      * totfeat=seqsfeatures.length; // Remove any features for this exact chain
@@ -197,21 +236,19 @@ public class PDBChain
     {
       status = PDBChain.IEASTATUS;
     }
-    SequenceFeature[] features = sequence.getSequenceFeatures();
-    if (features == null)
-    {
-      return null;
-    }
-    for (int i = 0; i < features.length; i++)
+
+    List<SequenceFeature> features = sequence.getSequenceFeatures();
+    for (SequenceFeature feature : features)
     {
-      if (features[i].getFeatureGroup() != null
-              && features[i].getFeatureGroup().equals(pdbid))
+      if (feature.getFeatureGroup() != null
+              && feature.getFeatureGroup().equals(pdbid))
       {
-        SequenceFeature tx = new SequenceFeature(features[i]);
-        tx.setBegin(1 + residues.elementAt(tx.getBegin() - offset).atoms
-                .elementAt(0).alignmentMapping);
-        tx.setEnd(1 + residues.elementAt(tx.getEnd() - offset).atoms
-                .elementAt(0).alignmentMapping);
+        int newBegin = 1 + residues.elementAt(feature.getBegin() - offset).atoms
+                .elementAt(0).alignmentMapping;
+        int newEnd = 1 + residues.elementAt(feature.getEnd() - offset).atoms
+                .elementAt(0).alignmentMapping;
+        SequenceFeature tx = new SequenceFeature(feature, newBegin, newEnd,
+                feature.getFeatureGroup(), feature.getScore());
         tx.setStatus(status
                 + ((tx.getStatus() == null || tx.getStatus().length() == 0)
                         ? ""
@@ -222,7 +259,6 @@ public class PDBChain
         }
       }
     }
-    return features;
   }
 
   /**
@@ -354,25 +390,25 @@ public class PDBChain
               && residues.lastElement().atoms
                       .get(0).resNumber == currAtom.resNumber)
       {
-        SequenceFeature sf = new SequenceFeature("INSERTION",
-                currAtom.resName + ":" + currAtom.resNumIns + " " + pdbid
-                        + id,
-                "", offset + count - 1, offset + count - 1, "PDB_INS");
+        String desc = currAtom.resName + ":" + currAtom.resNumIns + " "
+                + pdbid + id;
+        SequenceFeature sf = new SequenceFeature("INSERTION", desc, offset
+                + count - 1, offset + count - 1, "PDB_INS");
         resFeatures.addElement(sf);
         residues.lastElement().atoms.addAll(resAtoms);
       }
       else
       {
-
         // Make a new Residue object with the new atoms vector
         residues.addElement(new Residue(resAtoms, resNumber - 1, count));
 
         Residue tmpres = residues.lastElement();
         Atom tmpat = tmpres.atoms.get(0);
         // Make A new SequenceFeature for the current residue numbering
-        SequenceFeature sf = new SequenceFeature(RESNUM_FEATURE,
-                tmpat.resName + ":" + tmpat.resNumIns + " " + pdbid + id,
-                "", offset + count, offset + count, pdbid);
+        String desc = tmpat.resName
+                + ":" + tmpat.resNumIns + " " + pdbid + id;
+        SequenceFeature sf = new SequenceFeature(RESNUM_FEATURE, desc,
+                offset + count, offset + count, pdbid);
         resFeatures.addElement(sf);
         resAnnotation.addElement(new Annotation(tmpat.tfactor));
         // Keep totting up the sequence
@@ -558,6 +594,12 @@ public class PDBChain
   {
     SequenceI sq = mapping.getSequence();
     SequenceI dsq = sq;
+    if (sqmpping == null)
+    {
+      // SIFTS mappings are recorded in the StructureMapping object...
+
+      sqmpping = mapping.getSeqToPdbMapping();
+    }
     if (sq != null)
     {
       while (dsq.getDatasetSequence() != null)